Metagenomic Insights into the Composition and Function of Microbes Associated with the Rootzone of Datura inoxia

Abstract

The purpose of this paper is to elucidate the roles that microbes may be playing in the rootzone of the medicinal plant Daturainoxia. We hypothesized that the microbes associated with the Datura rootzone would be significantly different than the similar surrounding fields in composition and function. We also hypothesized that rhizospheric and endophytic microbes would be associated with similar metabolic functions to the plant rootzone they inhabited. The methods employed were microbial barcoding, tests of essential oils against antibiotic resistant bacteria and other soil bacterial isolates, 16S Next Generation Sequencing (NGS) metabarcoding, and Whole Genome Shotgun (WGS) taxonomic and functional analyses. A few of the main bacterial genera of interest that were differentially abundant in the Datura root microbiome were Flavobacterium (p = 0.007), Chitinophaga (p = 0.0007), Pedobacter (p = 6 × 10−5), Bradyhizobium (p = 1 × 10−8), and Paenibacillus (p = 1.46 × 10−6). There was significant evidence that the microbes associated with the Datura rootzone had elevated function related to bacterial chalcone synthase (p = 1.49 × 10−3) and permease genes (p < 0.003). There was some evidence that microbial functions in the Datura rootzone provided precursors to important plant bioactive molecules or were beneficial to plant growth. This is important because these compounds are phyto-protective antioxidants and are precursors to many aromatic bioactive compounds that are relevant to human health. In the context of known interactions, and current results, plants and microbes influence the flavonoid biosynthetic pathways of one other, in terms of the regulation of the phenylpropanoid pathway. This is the first study to focus on the microbial ecology of the Datura rootzone. There are possible biopharmaceutical and agricultural applications of the natural interplay that was discovered during this study of the Datura inoxia rhizosphere.

Metagenomics approaches to understanding soil health in environmental research - a review

“…The authors concluded that the obtained information provides a start for phytopathology studies and the recognition of microorganisms that colonize these exterior parts of plants (Su et al, 2022). Senn et al (2022) analyzed the composition and function of microorganisms associated with the radicular zone of the medicinal plant Datura inoxia, and found that the principal genera associated with the plant's rhizosphere were Flavobacterium, Pedobacter, and Paenibacilus, among others. Bacteria of the genus Flavobacterium are known to possess a tyrosine ammonia-lyase gene, which has been employed to optimize the production of aromatic compounds of pharmaceutical interest.…”

“…Bacteria of the genus Flavobacterium are known to possess a tyrosine ammonia-lyase gene, which has been employed to optimize the production of aromatic compounds of pharmaceutical interest. They also found precursors to vegetal growth with antioxidant and phytoprotective compounds (Senn et al, 2022). On the other hand, a study in 2021 performed a metagenomic analysis of promotor genes involved with vegetal growth and the carbon cycle in the rhizosphere of corn fields with different land use histories.…”

The known, unknown, and the intriguing about members of a critically endangered traditional medicinal plant genus Aconitum

“…This compound was also shown to have protective effects against b-amyloid induced neurotoxicity in vitro and requires more research in treating Alzheimer's disease. NAChRs are vital targets in the drug discovery field because of their role in several disorders such as Tourette's syndrome, anxiety, depression, smoking cessation, and irritable bowel syndrome (Leonard et al, 2000;Navarro et al, 2000;Tucci et al, 2003;Senn et al, 2022). Ligands of this receptor that specifically bind to nAChR are particularly significant for drug discovery.…”

Microbial abundance estimation and metagenomic studies of holcomb creosote superfund site soil sample

“…In applied soil science, shotgun metagenomics techniques have the benefit of amplifying sequences from throughout the genome, including coding sections, resulting in a high sequencing depth but at a greater cost. 16S Meta barcoding is a diagnostic technique for bacterial and archaeal identification used in clinical sciences and plant ecology (Senn et al 2022). Targeted 16S rRNA amplicons sequenced by a variety of methods are currently being used to examine the microbiota composition in detail.…”